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Update of Equipment usage UI

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This commit is contained in:
lwark
2025-06-27 13:32:36 -05:00
parent d8c3f3bbb2
commit 054345e3e1
11 changed files with 644 additions and 140 deletions
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187
src/submissions/backend/validators/pydant.py
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@@ -9,6 +9,8 @@ from dateutil.parser import parse
from dateutil.parser import ParserError
from typing import List, Tuple, Literal
from types import GeneratorType
import backend
from . import RSLNamer
from pathlib import Path
from tools import check_not_nan, convert_nans_to_nones, Report, Result, timezone
@@ -31,7 +33,11 @@ class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
def prevalidate(cls, data):
sql_fields = [k for k, v in cls._sql_object.__dict__.items() if isinstance(v, InstrumentedAttribute)]
output = {}
for key, value in data.items():
try:
items = data.items()
except AttributeError:
return data
for key, value in items:
new_key = key.replace("_", "")
if new_key in sql_fields:
output[new_key] = value
@@ -104,11 +110,14 @@ class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
def to_sql(self):
dicto = self.improved_dict(dictionaries=False)
logger.debug(f"Dicto: {dicto}")
sql, _ = self._sql_object().query_or_create(**dicto)
# sql, new = self._sql_object().query_or_create(**dicto)
sql, new = self._sql_object.query_or_create(**dicto)
if new:
logger.warning(f"Creating new {self._sql_object} with values:\n{pformat(dicto)}")
return sql
class PydReagent(BaseModel):
class PydReagent(PydBaseClass):
lot: str | None
reagentrole: str | None
expiry: date | datetime | Literal['NA'] | None = Field(default=None, validate_default=True)
@@ -269,6 +278,7 @@ class PydSample(PydBaseClass):
value = row_keys[value]
return value
class PydTips(BaseModel):
name: str
lot: str | None = Field(default=None)
@@ -277,6 +287,13 @@ class PydTips(BaseModel):
@field_validator('tiprole', mode='before')
@classmethod
def get_role_name(cls, value):
if isinstance(value, list):
output = []
for tiprole in value:
if isinstance(tiprole, TipRole):
tiprole = tiprole.name
return tiprole
value = output
if isinstance(value, TipRole):
value = value.name
return value
@@ -304,13 +321,21 @@ class PydEquipment(BaseModel, extra='ignore'):
asset_number: str
name: str
nickname: str | None
process: List[str] | None
equipmentrole: str | None
tips: List[PydTips] | None = Field(default=None)
# process: List[dict] | None
process: PydProcess | None
equipmentrole: str | PydEquipmentRole | None
tips: List[PydTips] | None = Field(default=[])
@field_validator('equipmentrole', mode='before')
@classmethod
def get_role_name(cls, value):
match value:
case list():
value = value[0]
case GeneratorType():
value = next(value)
case _:
pass
if isinstance(value, EquipmentRole):
value = value.name
return value
@@ -325,12 +350,24 @@ class PydEquipment(BaseModel, extra='ignore'):
value = convert_nans_to_nones(value)
if not value:
value = ['']
logger.debug(value)
try:
value = [item.strip() for item in value]
# value = [item.strip() for item in value]
value = next((PydProcess(**process.details_dict()) for process in value))
except AttributeError:
pass
return value
@field_validator('tips', mode='before')
@classmethod
def tips_to_pydantic(cls, value):
output = []
for tips in value:
if isinstance(tips, Tips):
tips = tips.to_pydantic()
output.append(tips)
return output
@report_result
def to_sql(self, procedure: Procedure | str = None, kittype: KitType | str = None) -> Tuple[
Equipment, ProcedureEquipmentAssociation]:
@@ -357,7 +394,7 @@ class PydEquipment(BaseModel, extra='ignore'):
# NOTE: Need to make sure the same association is not added to the procedure
try:
assoc, new = ProcedureEquipmentAssociation.query_or_create(equipment=equipment, procedure=procedure,
equipmentrole=self.equipmentrole, limit=1)
equipmentrole=self.equipmentrole, limit=1)
except TypeError as e:
logger.error(f"Couldn't get association due to {e}, returning...")
return None, None
@@ -1282,8 +1319,14 @@ class PydProcess(BaseModel, extra="allow"):
@classmethod
def enforce_list(cls, value):
if not isinstance(value, list):
return [value]
return value
value = [value]
output = []
for v in value:
if issubclass(v.__class__, BaseClass):
output.append(v.name)
else:
output.append(v)
return output
@report_result
def to_sql(self):
@@ -1356,7 +1399,28 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
plate_map: str | None = Field(default=None)
reagent: list | None = Field(default=[])
reagentrole: dict | None = Field(default={}, validate_default=True)
samples: List[PydSample] = Field(default=[])
sample: List[PydSample] = Field(default=[])
equipment: List[PydEquipment] = Field(default=[])
results: List[PydResults] | List[dict] = Field(default=[])
@field_validator("name", "technician", "kittype", mode="before")
@classmethod
def convert_to_dict(cls, value):
if isinstance(value, str):
value = dict(value=value, missing=False)
return value
@field_validator("proceduretype", mode="before")
@classmethod
def lookup_proceduretype(cls, value):
match value:
case dict():
value = ProcedureType.query(name=value['name'])
case str():
value = ProcedureType.query(name=value)
case _:
pass
return value
@field_validator("name")
@classmethod
@@ -1378,25 +1442,41 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
@classmethod
def rescue_possible_kits(cls, value, values):
if not value:
if values.data['proceduretype']:
value = [kittype.name for kittype in values.data['proceduretype'].kittype]
try:
if values.data['proceduretype']:
value = [kittype.__dict__['name'] for kittype in values.data['proceduretype'].kittype]
except KeyError:
pass
return value
@field_validator("name", "technician", "kittype")
@classmethod
def set_colour(cls, value):
if value["missing"]:
value["colour"] = "FE441D"
else:
value["colour"] = "6ffe1d"
try:
if value["missing"]:
value["colour"] = "FE441D"
else:
value["colour"] = "6ffe1d"
except KeyError:
pass
return value
@field_validator("reagentrole")
@classmethod
def rescue_reagentrole(cls, value, values):
if not value:
if values.data['kittype']['value'] != cls.model_fields['kittype'].default['value']:
kittype = KitType.query(name=values.data['kittype']['value'])
match values.data['kittype']:
case dict():
if "value" in values.data['kittype'].keys():
roi = values.data['kittype']['value']
elif "name" in values.data['kittype'].keys():
roi = values.data['kittype']['name']
else:
raise KeyError(f"Couldn't find kittype name in the dictionary: {values.data['kittype']}")
case str():
roi = values.data['kittype']
if roi != cls.model_fields['kittype'].default['value']:
kittype = KitType.query(name=roi)
value = {item.name: item.reagent for item in kittype.reagentrole}
return value
@@ -1413,6 +1493,19 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
self.kittype['value'] = kittype
self.possible_kits.insert(0, self.possible_kits.pop(self.possible_kits.index(kittype)))
def update_kittype_equipmentroles(self, kittype: str | KitType):
if kittype == self.__class__.model_fields['kittype'].default['value']:
return
if isinstance(kittype, str):
kittype_obj = KitType.query(name=kittype)
try:
self.equipment = {item.name: item.get_reagents(kittype=kittype_obj) for item in
kittype_obj.get_reagents(proceduretype=self.proceduretype)}
except AttributeError:
self.reagentrole = {}
self.kittype['value'] = kittype
self.possible_kits.insert(0, self.possible_kits.pop(self.possible_kits.index(kittype)))
def update_samples(self, sample_list: List[dict]):
logger.debug(f"Incoming sample_list:\n{pformat(sample_list)}")
for sample_dict in sample_list:
@@ -1425,7 +1518,8 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
(item for item in self.samples if item.sample_id.upper() == sample_dict['sample_id'].upper()))
except StopIteration:
# NOTE: Code to check for added controls.
logger.debug(f"Sample not found by name: {sample_dict['sample_id']}, checking row {row} column {column}")
logger.debug(
f"Sample not found by name: {sample_dict['sample_id']}, checking row {row} column {column}")
try:
sample = next(
(item for item in self.samples if item.row == row and item.column == column))
@@ -1441,7 +1535,12 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
def to_sql(self):
from backend.db.models import RunSampleAssociation, ProcedureSampleAssociation
# results = []
# for result in self.results:
# result, _ = result.to_sql()
sql = super().to_sql()
logger.debug(f"Initial PYD: {pformat(self.__dict__)}")
# sql.results = [result.to_sql() for result in self.results]
if self.run:
sql.run = self.run
if self.proceduretype:
@@ -1450,27 +1549,37 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
start_index = max([item.id for item in ProcedureSampleAssociation.query()]) + 1
except ValueError:
start_index = 1
relevant_samples = [sample for sample in self.samples if not sample.sample_id.startswith("blank_") and not sample.sample_id == ""]
relevant_samples = [sample for sample in self.sample if
not sample.sample_id.startswith("blank_") and not sample.sample_id == ""]
logger.debug(f"start index: {start_index}")
assoc_id_range = range(start_index, start_index + len(relevant_samples)+1)
assoc_id_range = range(start_index, start_index + len(relevant_samples) + 1)
logger.debug(f"Association id range: {assoc_id_range}")
for iii, sample in enumerate(relevant_samples):
sample_sql = sample.to_sql()
if sql.run:
if sample_sql not in sql.run.sample:
logger.debug(f"sample {sample_sql} not found in {sql.run.sample}")
run_assoc = RunSampleAssociation(sample=sample_sql, run=self.run, row=sample.row, column=sample.column)
run_assoc = RunSampleAssociation(sample=sample_sql, run=self.run, row=sample.row,
column=sample.column)
else:
logger.debug(f"sample {sample_sql} found in {sql.run.sample}")
proc_assoc = ProcedureSampleAssociation(new_id=assoc_id_range[iii], procedure=sql, sample=sample_sql, row=sample.row, column=sample.column)
if sample_sql not in sql.sample:
proc_assoc = ProcedureSampleAssociation(new_id=assoc_id_range[iii], procedure=sql, sample=sample_sql,
row=sample.row, column=sample.column)
if self.kittype['value'] not in ["NA", None, ""]:
kittype = KitType.query(name=self.kittype['value'], limit=1)
if kittype:
sql.kittype = kittype
for equipment in self.equipment:
equip = Equipment.query(name=equipment.name)
if equip not in sql.equipment:
equip_assoc = ProcedureEquipmentAssociation(equipment=equip, procedure=sql, equipmentrole=equip.equipmentrole[0])
process = equipment.process.to_sql()
equip_assoc.process = process
logger.debug(f"Output sql: {[pformat(item.__dict__) for item in sql.procedureequipmentassociation]}")
return sql, None
class PydClientSubmission(PydBaseClass):
# sql_object: ClassVar = ClientSubmission
@@ -1549,15 +1658,34 @@ class PydClientSubmission(PydBaseClass):
class PydResults(PydBaseClass, arbitrary_types_allowed=True):
results: dict = Field(default={})
results_type: str = Field(default="NA")
img: None | bytes = Field(default=None)
parent: Procedure|ProcedureSampleAssociation|None = Field(default=None)
parent: Procedure | ProcedureSampleAssociation | None = Field(default=None)
date_analyzed: datetime | None = Field(default=None)
@field_validator("date_analyzed")
@classmethod
def set_today(cls, value):
match value:
case str():
value = datetime.strptime(value, "%Y-%m-%d %H:%M:%S")
case datetime():
pass
case _:
value = datetime.now()
return value
def to_sql(self):
sql = Results(results_type=self.results_type, result=self.results)
sql.image = self.img
sql, _ = Results.query_or_create(results_type=self.results_type, result=self.results)
try:
check = sql.image
except FileNotFoundError:
check = False
if not check:
sql.image = self.img
if not sql.date_analyzed:
sql.date_analyzed = self.date_analyzed
match self.parent:
case ProcedureSampleAssociation():
sql.sampleprocedureassociation = self.parent
@@ -1566,4 +1694,3 @@ class PydResults(PydBaseClass, arbitrary_types_allowed=True):
case _:
logger.error("Improper association found.")
return sql